Publications

  1. Sankaranarayanan S, Balan J, Walsh JR, Wu Y, Minnich S, Piazza A, Osborne C, Oliver GR, Lesko J, Bates KL, Khezeli K, Block DR, DiGuardo M, Kreuter J, O'Horo JC, Kalantari J, Klee EW, Salama ME, Kipp B, Morice WG, Jenkinson G. COVID-19 Mortality Prediction From Deep Learning in a Large Multistate Electronic Health Record and Laboratory Information System Data Set: Algorithm Development and Validation. J Med Internet Res. 2021 Sep 28; 23(9):e30157.
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  2. DeVoe E, Oliver GR, Zenka R, Blackburn PR, Cousin MA, Boczek NJ, Kocher JA, Urrutia R, Klee EW, Zimmermann MT. P(2)T(2): Protein Panoramic annoTation Tool for the interpretation of protein coding genetic variants. JAMIA Open. 2021 Jul; 4 (3):ooab065 Epub 2021 Aug 07
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  3. Klee EW, Cousin MA, Pinto E Vairo F, Morales-Rosado JA, Macke EL, Jenkinson WG, Ferrer A, Schultz-Rogers LE, Olson RJ, Oliver GR, Sigafoos AN, Schwab TL, Zimmermann MT, Urrutia RA, Kaiwar C, Gupta A, Blackburn PR, Boczek NJ, Prochnow CA, Lowy RJ, Mulvihill LA, McAllister TM, Aoudia SL, Kruisselbrink TM, Gunderson LB, Kemppainen JL, Fisher LJ, Tarnowski JM, Hager MM, Kroc SA, Bertsch NL, Agre KE, Jackson JL, Macklin-Mantia SK, Murphree MI, Rust LM, Summer Bolster JM, Beck SA, Atwal PS, Ellingson MS, Barnett SS, Rasmussen KJ, Lahner CA, Niu Z, Hasadsri L, Ferber MJ, Marcou CA, Clark KJ, Pichurin PN, Deyle DR, Morava-Kozicz E, Gavrilova RH, Dhamija R, Wierenga KJ, Lanpher BC, Babovic-Vuksanovic D, Farrugia G, Schimmenti LA, Stewart AK, Lazaridis KN. Impact of integrated translational research on clinical exome sequencing. Genet Med. 2021 Mar; 23 (3):498-507 Epub 2020 Nov 04
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  4. Oliver GR, Marcano-Bonilla S, Quist J, Tolosa EJ, Iguchi E, Swanson AA, Hoppman NL, Schwab T, Sigafoos A, Prodduturi N, Voss JS, Knight SM, Zhang J, Fadra N, Urrutia R, Zimmerman M, Egan JB, Bilyeu AG, Jen J, Veras E, Al-Safi R, Block M, Kerr S, Fernandez-Zapico ME, Schoolmeester JK, Klee EW. LPCAT1-TERT fusions are uniquely recurrent in epithelioid trophoblastic tumors and positively regulate cell growth. PLoS One. 2021; 16(5):e0250518. Epub 2021 May 25.
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  5. Balan J, Jenkinson G, Nair A, Saha N, Koganti T, Voss J, Zysk C, Barr Fritcher EG, Ross CA, Giannini C, Raghunathan A, Kipp BR, Jenkins R, Ida C, Halling KC, Blackburn PR, Dasari S, Oliver GR, Klee EW. SeekFusion - A Clinically Validated Fusion Transcript Detection Pipeline for PCR-Based Next-Generation Sequencing of RNA. Front Genet. 2021; 12:739054. Epub 2021 Oct 22.
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  6. Jenkinson G, Li YI, Basu S, Cousin MA, Oliver GR, Klee EW. LeafCutterMD: an algorithm for outlier splicing detection in rare diseases. Bioinformatics. 2020 Nov 1; 36 (17):4609-4615
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  7. Morales-Rosado JA, Macke EL, Cousin MA, Oliver GR, Dhamija R, Klee EW. Interpretation challenges of novel dual-class missense and splice-impacting variant in POLR3A-related late-onset hereditary spastic ataxia. Mol Genet Genomic Med. 2020 Sep; 8 (9):e1341 Epub 2020 June 29
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  8. Oliver GR, Jenkinson G, Klee EW. Computational Detection of Known Pathogenic Gene Fusions in a Normal Tissue Database and Implications for Genetic Disease Research. Front Genet. 2020; 11:173 Epub 2020 Feb 28
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  9. Zepeda-Mendoza CJ, Cousin MA, Basu S, Jenkinson G, Oliver G, Pittock ST, Baughn LB, Klee EW, Babovic-Vuksanovic D. An intragenic duplication of TRPS1 leading to abnormal transcripts and causing trichorhinophalangeal syndrome type I. Cold Spring Harb Mol Case Stud. 2019 Dec; 5 (6) Epub 2019 Dec 13
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  10. Mangaonkar AA, Patnaik MM, Oliver GR, Rao KW, Kaiser-Rogers K, Davila JI, Fadra N, Wehrs RN, Elliott MA, Greipp PT, Halling KC, Van Dyke DL. Multiple isodicentric Y chromosomes in myeloid malignancies: a unique cytogenetic entity and potential therapeutic target. Leuk Lymphoma 2019 Mar; 60 (3):821-824 Epub 2018 Aug 30
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  11. Oliver GR, Blackburn PR, Ellingson MS, Conboy E, Pinto E Vairo F, Webley M, Thorland E, Ferber M, Van Hul E, van der Werf IM, Wuyts W, Babovic-Vuksanovic D, Klee EW. RNA-Seq detects a SAMD12-EXT1 fusion transcript and leads to the discovery of an EXT1 deletion in a child with multiple osteochondromas. Mol Genet Genomic Med. 2019 Mar; 7 (3):e00560 Epub 2019 Jan 10
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  12. Oliver GR, Tang X, Schultz-Rogers LE, Vidal-Folch N, Jenkinson WG, Schwab TL, Gaonkar K, Cousin MA, Nair A, Basu S, Chanana P, Oglesbee D, Klee EW. A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease. PLoS One. 2019; 14 (10):e0223337 Epub 2019 Oct 02
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  13. Boczek NJ, Hopp K, Benoit L, Kraft D, Cousin MA, Blackburn PR, Madsen CD, Oliver GR, Nair AA, Na J, Bianchi DW, Beek G, Harris PC, Pichurin P, Klee EW. Characterization of three ciliopathy pedigrees expands the phenotype associated with biallelic C2CD3 variants. Eur J Hum Genet. 2018 Dec; 26 (12):1797-1809 Epub 2018 Aug 10
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  14. Winters JL, Davila JI, McDonald AM, Nair AA, Fadra N, Wehrs RN, Thomas BC, Balcom JR, Jin L, Wu X, Voss JS, Klee EW, Oliver GR, Graham RP, Neff JL, Rumilla KM, Aypar U, Kipp BR, Jenkins RB, Jen J, Halling KC. Development and Verification of an RNA Sequencing (RNA-Seq) Assay for the Detection of Gene Fusions in Tumors. J Mol Diagn. 2018 Jul; 20(4):495-511. Epub 2018 Jun 19.
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  15. Lomberk G, Blum Y, Nicolle R, Nair A, Gaonkar KS, Marisa L, Mathison A, Sun Z, Yan H, Elarouci N, Armenoult L, Ayadi M, Ordog T, Lee JH, Oliver G, Klee E, Moutardier V, Gayet O, Bian B, Duconseil P, Gilabert M, Bigonnet M, Garcia S, Turrini O, Delpero JR, Giovannini M, Grandval P, Gasmi M, Secq V, De Reynies A, Dusetti N, Iovanna J, Urrutia R. Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes. Nat Commun. 2018 May 17; 9 (1):1978
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  16. Cousin MA, Smith MJ, Sigafoos AN, Jin JJ, Murphree MI, Boczek NJ, Blackburn PR, Oliver GR, Aleff RA, Clark KJ, Wieben ED, Joshi AY, Pichurin PN, Abraham RS, Klee EW. Utility of DNA, RNA, Protein, and Functional Approaches to Solve Cryptic Immunodeficiencies. J Clin Immunol. 2018 Apr; 38 (3):307-319 Epub 2018 Apr 18
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  17. Zimmermann MT, Urrutia R, Cousin MA, Oliver GR, Klee EW. Assessing Human Genetic Variations in Glucose Transporter SLC2A10 and Their Role in Altering Structural and Functional Properties. Front Genet. 2018; 9:276 Epub 2018 July 25
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  18. Davila JI, Starr JS, Attia S, Wang C, Knudson RA, Necela BM, Sarangi V, Sun Z, Ren Y, Casler JD, Menke DM, Oliver GR, Joseph RW, Copland JA, Parker AS, Kocher JA, Thompson EA, Smallridge RC, Asmann YW. Comprehensive Genomic Profiling of a Rare Thyroid Follicular Dendritic Cell Sarcoma. Rare Tumors. 2017 Jul 3; 9 (2):6834 Epub 2017 Sept 15
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  19. Cousin MA, Zimmermann MT, Mathison AJ, Blackburn PR, Boczek NJ, Oliver GR, Lomberk GA, Urrutia RA, Deyle DR, Klee EW. Functional validation reveals the novel missense V419L variant in TGFBR2 associated with Loeys-Dietz syndrome (LDS) impairs canonical TGF-beta signaling. Cold Spring Harb Mol Case Stud. 2017 Jul; 3 (4) Epub 2017 July 05
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  20. Bryce AH, Egan JB, Borad MJ, Stewart AK, Nowakowski GS, Chanan-Khan A, Patnaik MM, Ansell SM, Banck MS, Robinson SI, Mansfield AS, Klee EW, Oliver GR, McCormick JB, Huneke NE, Tagtow CM, Jenkins RB, Rumilla KM, Kerr SE, Kocher JA, Beck SA, Fernandez-Zapico ME, Farrugia G, Lazaridis KN, McWilliams RR. Experience with precision genomics and tumor board, indicates frequent target identification, but barriers to delivery. Oncotarget. 2017 Apr 18; 8 (16):27145-27154
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  21. Blackburn PR, Tischer A, Zimmermann MT, Kemppainen JL, Sastry S, Knight Johnson AE, Cousin MA, Boczek NJ, Oliver G, Misra VK, Gavrilova RH, Lomberk G, Auton M, Urrutia R, Klee EW. A Novel Kleefstra Syndrome-associated Variant That Affects the Conserved TPLX Motif within the Ankyrin Repeat of EHMT1 Leads to Abnormal Protein Folding. J Biol Chem. 2017 Mar 3; 292 (9):3866-3876 Epub 2017 Jan 05
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  22. Zimmermann MT, Urrutia R, Oliver GR, Blackburn PR, Cousin MA, Bozeck NJ, Klee EW. Molecular modeling and molecular dynamic simulation of the effects of variants in the TGFBR2 kinase domain as a paradigm for interpretation of variants obtained by next generation sequencing. PLoS One. 2017; 12 (2):e0170822 Epub 2017 Feb 09
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  23. Egan JB, Marks DL, Hogenson TL, Vrabel AM, Sigafoos AN, Tolosa EJ, Carr RM, Safgren SL, Hesles EE, Almada LL, Romecin-Duran PA, Iguchi E, Ala'Aldeen A, Kocher JA, Oliver GR, Prodduturi N, Mead DW, Hossain A, Huneke NE, Tagtow CM, Ailawadhi S, Ansell SM, Banck MS, Bryce AH, Carballido EM, Chanan-Khan AA, Curtis KK, Resnik E, Gawryletz CD, Go RS, Halfdanarson TR, Ho TH, Joseph RW, Kapoor P, Mansfield AS, Meurice N, Nageswara Rao AA, Nowakowski GS, Pardanani A, Parikh SA, Cheville JC, Feldman AL, Ramanathan RK, Robinson SI, Tibes R, Finnes HD, McCormick JB, McWilliams RR, Jatoi A, Patnaik MM, Silva AC, Wieben ED, McAllister TM, Rumilla KM, Kerr SE, Lazaridis KN, Farrugia G, Stewart AK, Clark KJ, Kennedy EJ, Klee EW, Borad MJ, Fernandez-Zapico ME. Molecular Modeling and Functional Analysis of Exome Sequencing-Derived Variants of Unknown Significance Identify a Novel, Constitutively Active FGFR2 Mutant in Cholangiocarcinoma. JCO Precis Oncol. 2017; 2017 Epub 2017 Aug 01
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  24. Oliver GR, Zimmermann MT, Klee EW, Urrutia RA. "The molecule's the thing:" the promise of molecular modeling and dynamic simulations in aiding the prioritization and interpretation of genomic testing results. F1000Res. 2016; 5:766 Epub 2016 Apr 27
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  25. Tibes R, Al-Kali A, Oliver GR, Delman DH, Hansen N, Bhagavatula K, Mohan J, Rakhshan F, Wood T, Foran JM, Mesa RA, Bogenberger JM. The Hedgehog pathway as targetable vulnerability with 5-azacytidine in myelodysplastic syndrome and acute myeloid leukemia. J Hematol Oncol. 2015 Oct 20; 8:114
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  26. Hart SN, Moore RM, Zimmermann MT, Oliver GR, Egan JB, Bryce AH, Kocher JA. PANDA: pathway and annotation explorer for visualizing and interpreting gene-centric data. PeerJ. 2015; 3:e970 Epub 2015 May 19
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  27. Oliver GR, Hart SN, Klee EW. Bioinformatics for clinical next generation sequencing. Clin Chem. 2015 Jan; 61 (1):124-35 Epub 2014 Dec 01
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  28. Wang C, Evans JM, Bhagwate AV, Prodduturi N, Sarangi V, Middha M, Sicotte H, Vedell PT, Hart SN, Oliver GR, Kocher JP, Maurer MJ, Novak AJ, Slager SL, Cerhan JR, Asmann YW. PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data. Bioinformatics. 2014 Sep 15; 30 (18):2678-80 Epub 2014 May 29
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  29. Borad MJ, Champion MD, Egan JB, Liang WS, Fonseca R, Bryce AH, McCullough AE, Barrett MT, Hunt K, Patel MD, Young SW, Collins JM, Silva AC, Condjella RM, Block M, McWilliams RR, Lazaridis KN, Klee EW, Bible KC, Harris P, Oliver GR, Bhavsar JD, Nair AA, Middha S, Asmann Y, Kocher JP, Schahl K, Kipp BR, Barr Fritcher EG, Baker A, Aldrich J, Kurdoglu A, Izatt T, Christoforides A, Cherni I, Nasser S, Reiman R, Phillips L, McDonald J, Adkins J, Mastrian SD, Placek P, Watanabe AT, Lobello J, Han H, Von Hoff D, Craig DW, Stewart AK, Carpten JD. Integrated genomic characterization reveals novel, therapeutically relevant drug targets in FGFR and EGFR pathways in sporadic intrahepatic cholangiocarcinoma. PLoS Genet. 2014 Feb; 10 (2):e1004135 Epub 2014 Feb 13
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  30. Plebani R, Oliver GR, Trerotola M, Guerra E, Cantanelli P, Apicella L, Emerson A, Albiero A, Harkin PD, Kennedy RD, Alberti S. Long-range transcriptome sequencing reveals cancer cell growth regulatory chimeric mRNA. Neoplasia. 2012 Nov; 14 (11):1087-96
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  31. Oliver GR. Considerations for clinical read alignment and mutational profiling using next-generation sequencing. F1000Res. 2012; 1:2 Epub 2012 July 16
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  32. Kennedy RD, Bylesjo M, Kerr P, Davison T, Black JM, Kay EW, Holt RJ, Proutski V, Ahdesmaki M, Farztdinov V, Goffard N, Hey P, McDyer F, Mulligan K, Mussen J, O'Brien E, Oliver G, Walker SM, Mulligan JM, Wilson C, Winter A, O'Donoghue D, Mulcahy H, O'Sullivan J, Sheahan K, Hyland J, Dhir R, Bathe OF, Winqvist O, Manne U, Shanmugam C, Ramaswamy S, Leon EJ, Smith WI, McDermott U, Wilson RH, Longley D, Marshall J, Cummins R, Sargent DJ, Johnston PG, Harkin DP. Development and independent validation of a prognostic assay for stage II colon cancer using formalin-fixed paraffin-embedded tissue. J Clin Oncol. 2011 Dec 10; 29(35):4620-6. Epub 2011 Nov 07.
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  33. Allen WL, Jithesh PV, Oliver GR, Proutski I, Longley DB, Lenz HJ, Proutski V, Harkin P, Johnston PG. The colorectal cancer disease-specific transcriptome may facilitate the discovery of more biologically and clinically relevant information. BMC Cancer. 2010 Dec 20; 10:687
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  34. Grigoriadis A, Oliver GR, Tanney A, Kendrick H, Smalley MJ, Jat P, Neville AM. Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues. BMC Genomics. 2009 Jul 17; 10:324 Epub 2009 July 17
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  35. Tanney A, Oliver GR, Farztdinov V, Kennedy RD, Mulligan JM, Fulton CE, Farragher SM, Field JK, Johnston PG, Harkin DP, Proutski V, Mulligan KA. Generation of a non-small cell lung cancer transcriptome microarray. BMC Med Genomics. 2008 May 30; 1:20
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  36. Smith TK, Oliver GR, Hennig GW, O'Shea DM, Vanden Berghe P, Kang SH, Spencer NJ. A smooth muscle tone-dependent stretch-activated migrating motor pattern in isolated guinea-pig distal colon. J Physiol. 2003 Sep 15; 551 (Pt 3):955-69 Epub 2003 July 07
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